Contacts of the strand formed by residues 47 - 59 (chain B) in PDB entry 3U8M
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLU 47 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B GLU* 4.2 0.5 - - - +
41B VAL* 3.7 0.9 - - - -
42B ASN* 2.9 31.1 + - + +
45B THR* 3.3 33.7 + - - +
46B ASN* 1.3 83.4 - - - +
48B VAL* 1.3 65.8 + - - +
92B ILE* 3.5 29.5 - - + +
120B ARG* 4.4 13.7 + - - -
121B PHE 3.2 7.4 - - - +
122B SER* 4.9 4.0 - - - -
125B VAL* 3.9 0.6 - - - +
39C LEU* 3.8 31.1 - - + +
118C ARG* 5.5 2.0 + - - -
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Residues in contact with VAL 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ILE* 5.3 0.9 - - + -
40B GLU 3.4 4.9 - - - +
41B VAL* 4.0 20.4 - - + -
47B GLU* 1.3 79.0 - - - +
49B ASP* 1.3 60.8 + - - +
50B VAL* 4.0 19.7 - - + -
119B GLN 4.0 0.5 - - - +
120B ARG* 3.1 7.5 - - - +
121B PHE* 2.8 39.8 + - + +
123B CYS* 3.7 24.5 - - - -
125B VAL* 3.5 23.1 - - + -
136B CYS* 3.9 7.6 - - - -
199B LEU* 6.5 0.2 - - + -
201B PHE* 4.1 13.9 - - + -
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Residues in contact with ASP 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ILE* 3.8 2.1 - - - +
39B LEU* 2.9 30.7 + - + +
40B GLU* 2.7 38.2 + - + +
48B VAL* 1.3 73.6 - - - +
50B VAL* 1.3 64.7 + - - +
118B ARG* 2.9 51.0 + - - +
119B GLN 3.9 5.2 - - - +
120B ARG* 3.7 22.7 - - + +
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Residues in contact with VAL 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B PHE* 3.7 33.2 - - + -
37B ASN 3.7 8.3 - - - +
38B ILE* 4.7 13.9 - - + -
39B LEU* 5.4 0.2 - - - -
48B VAL* 4.0 24.7 - - + -
49B ASP* 1.3 80.4 + - - +
51B VAL* 1.3 68.6 + - - +
52B PHE* 3.7 14.3 - - + -
117B ILE 3.6 0.7 - - - +
118B ARG* 3.3 4.5 - - - +
119B GLN 3.0 36.4 + - - +
121B PHE* 4.3 12.8 - - + -
136B CYS* 6.0 0.2 - - - -
138B ILE* 5.3 2.2 - - + -
199B LEU* 4.8 9.9 - - + -
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Residues in contact with VAL 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A ALA 5.0 4.7 - - - +
92A ILE* 4.7 8.3 - - + -
35B PHE 3.9 0.2 - - - -
36B ILE* 2.9 38.7 + - + -
37B ASN* 3.0 23.0 + - + +
39B LEU* 3.8 24.2 - - + -
50B VAL* 1.3 82.0 - - - +
52B PHE* 1.3 64.1 + - - +
98B LEU* 4.2 10.8 - - + -
116B SER* 3.8 19.7 - - - +
117B ILE 3.1 5.4 - - - +
118B ARG* 3.7 22.0 - - + -
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Residues in contact with PHE 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B LEU* 3.6 32.8 - - + -
34B LYS 3.4 13.2 - - - +
35B PHE* 4.0 18.8 - + + -
36B ILE* 4.0 1.8 - - - -
50B VAL* 3.7 15.5 - - + -
51B VAL* 1.3 79.8 - - - +
53B TRP* 1.3 66.8 + - - +
54B GLN* 3.5 28.8 + - + -
116B SER* 4.4 0.2 - - - -
117B ILE* 2.7 65.0 + - + -
119B GLN* 3.9 16.2 - - + -
121B PHE* 3.7 28.9 - + - -
138B ILE* 5.6 0.2 - - + -
140B ILE* 5.2 2.2 - - + -
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Residues in contact with TRP 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A TYR* 4.0 23.4 + + + -
143A TRP* 3.3 35.7 - + - -
185A TYR* 4.3 23.1 - + + -
187A CYS* 6.1 0.4 - - + -
33B LEU* 3.5 5.0 - - - -
34B LYS* 2.8 41.7 + - + +
36B ILE* 3.5 29.1 - - + +
52B PHE* 1.3 71.4 - - - +
54B GLN* 1.3 58.5 + - - +
55B GLN 3.5 2.3 + - - -
114B MET* 3.8 40.2 - - + -
115B PRO 3.3 5.2 - - - +
116B SER* 3.4 25.4 + - - -
164B TYR* 3.8 41.1 - + + -
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Residues in contact with GLN 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B VAL* 4.4 8.3 - - + -
32B SER 3.9 2.2 - - - -
33B LEU* 3.8 14.4 - - + -
52B PHE* 3.5 27.2 + - + -
53B TRP* 1.3 71.2 - - - +
55B GLN* 1.3 57.1 + - - +
56B THR* 3.3 16.5 + - - +
86B LEU* 4.3 24.4 + - - +
113B TYR 3.2 14.4 - - - +
114B MET* 4.0 2.2 - - - -
115B PRO* 2.9 26.4 + - + +
117B ILE* 3.9 22.6 - - + +
119B GLN* 5.4 1.2 - - - +
140B ILE* 4.0 16.8 - - - +
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Residues in contact with GLN 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A CYS* 3.9 22.0 - - - +
30B SER* 3.5 1.4 + - - +
31B VAL* 3.3 6.1 - - - +
32B SER* 2.9 47.3 + - - +
34B LYS* 3.3 25.2 + - + +
53B TRP 3.5 1.6 + - - -
54B GLN* 1.3 70.4 - - - +
56B THR* 1.3 61.0 + - - +
57B THR* 5.6 4.3 + - - +
112B LEU* 3.8 17.3 - - + -
114B MET* 3.5 25.9 - - - +
155B THR* 2.8 37.0 + - - +
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Residues in contact with THR 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B VAL* 3.7 23.1 - - + -
30B SER 3.2 3.8 - - - +
31B VAL* 4.6 0.7 - - + +
54B GLN* 3.3 26.7 + - - +
55B GLN* 1.3 76.9 + - - +
57B THR* 1.3 63.6 + - - +
58B TRP* 3.7 23.7 - - + -
83B VAL* 6.1 0.7 - - + -
84B PRO* 4.1 3.8 - - + -
86B LEU* 3.9 15.8 - - + +
111B VAL 3.7 0.9 - - - +
112B LEU* 3.5 7.1 - - - +
113B TYR* 2.7 45.6 + - - -
115B PRO* 5.3 0.2 - - - +
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Residues in contact with THR 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B ALA 3.7 1.4 - - - +
29B VAL* 3.3 1.9 - - - +
30B SER* 2.7 60.4 + - - +
55B GLN* 5.6 4.6 + - - +
56B THR* 1.3 76.7 + - - +
58B TRP* 1.3 67.9 - - - +
110B GLU* 3.8 23.3 + - - +
111B VAL 3.3 10.2 + - - -
112B LEU* 3.8 15.1 - - - +
155B THR* 6.0 0.2 - - - -
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Residues in contact with TRP 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B PRO* 4.8 0.2 - - + -
27B VAL* 4.1 9.2 - - + -
28B ALA 3.7 15.9 - - - +
29B VAL* 4.3 5.8 - - + -
56B THR* 3.7 32.3 - - + -
57B THR* 1.3 84.7 - - - +
59B SER* 1.3 75.0 + - - +
60B ASP* 4.2 6.5 - - + +
63B LEU* 5.9 0.2 - - - +
81B LEU* 5.2 2.5 - - + -
82B TRP* 3.2 47.9 + + - -
83B VAL* 4.2 15.9 - - + -
84B PRO* 3.6 27.6 - - + -
103B ALA* 5.6 0.9 - - + -
110B GLU* 3.6 10.0 - - - +
111B VAL* 2.8 65.3 + - + +
113B TYR* 4.2 13.9 - - + -
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Residues in contact with SER 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B PRO* 3.8 18.2 - - - +
22B GLN* 4.4 10.7 - - - +
27B VAL* 4.1 8.6 - - - +
28B ALA 4.5 3.6 + - - -
58B TRP* 1.3 80.5 - - - +
60B ASP* 1.3 60.1 + - - +
61B ARG* 3.3 31.8 + - - -
108B ASP 4.6 0.9 + - - -
109B GLY 3.6 11.2 + - - -
110B GLU* 4.5 11.7 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il